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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A (ONE MOLECULE IN THE ASYMMETRIC UNIT)
 
Authors :  P. S. Gandhi, M. J. Page, Z. Chen, L. Bush-Pelc, E. Di Cera
Date :  22 May 09  (Deposition) - 07 Jul 09  (Release) - 15 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine Protease, Acute Phase, Blood Coagulation, Calcium, Cleavage On Pair Of Basic Residues, Disulfide Bond, Gamma- Carboxyglutamic Acid, Glycoprotein, Hydrolase, Kringle, Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. S. Gandhi, M. J. Page, Z. Chen, L. Bush-Pelc, E. Di Cera
Mechanism Of The Anticoagulant Activity Of Thrombin Mutant W215A/E217A.
J. Biol. Chem. V. 284 24098 2009
PubMed-ID: 19586901  |  Reference-DOI: 10.1074/JBC.M109.025403
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THROMBIN LIGHT CHAIN
    ChainsA
    EC Number3.4.21.5
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellBHK CELLS
    Expression System OrganBABY HAMSTER KIDNEY
    Expression System Taxid10029
    Expression System VectorHPC4-PNUT
    GeneF2, CF2
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCOAGULATION FACTOR II
 
Molecule 2 - THROMBIN HEAVY CHAIN
    ChainsB
    EC Number3.4.21.5
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellBHK CELLS
    Expression System OrganBABY HAMSTER KIDNEY
    Expression System Taxid10029
    Expression System VectorHPC4-PNUT
    GeneF2, CF2
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCOAGULATION FACTOR II

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3HK3)

(-) Sites  (0, 0)

(no "Site" information available for 3HK3)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:1 -B:122
2B:42 -B:58
3B:168 -B:182
4B:191 -B:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:36A-Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HK3)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.THRB_MOUSE361-615  1B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.THRB_MOUSE399-404  1B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.THRB_MOUSE559-570  1B:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 3HK3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:30
 aligned with THRB_MOUSE | P19221 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:30
                                   339       349       359
          THRB_MOUSE    330 EADCGLRPLFEKKSLKDTTEKELLDSYIDG  359
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .........hhhhh....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------ PROSITE (1)
                PROSITE (2) ------------------------------ PROSITE (2)
                 Transcript ------------------------------ Transcript
                3hk3 A   1C EADCGLRPLFEKKSLKDTTEKELLDSYIDG  14M
                            |||      7       14C|||||||14M
                            |||            14A||||||14J|||
                           1C||             14B||||||14K||
                            1B|              14C||||||14L|
                             1A               14D||||| 14M
                                               14E||||    
                                                14F|||    
                                                 14G||    
                                                  14H|    
                                                   14I    

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with THRB_MOUSE | P19221 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:258
                                   370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610        
          THRB_MOUSE    361 IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLLVRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCLPDKQTVTSLLRAGYKGRVTGWGNLRETWTTNINEIQPSVLQVVNLPIVERPVCKASTRIRITDNMFCAGFKVNDTKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRKGKYGFYTHVFRLKRWIQKVIDQFG  618
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3hk3B01     3hk3B02 B:28-120,B:233-245 Trypsin-like serine proteases                                                 3hk3B01 B:16-27,B:121-232 Tryps      in-like serine proteases                                                                  3hk3B02      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee....eeeeeeee....eeeehhhh.eehhhhee.hhh.eeeee.............eeeeeeeeee..............eeeee................hhhhhhhhh....eeeeee........------......eeeeee..hhhhhhhh........eeee............hhhhh..eeeee......eeeeeeeee..hhhhh...eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 361-615                                                                                                                                                                                                                    --- PROSITE (1)
                PROSITE (2) --------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3hk3 B   16 IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLLVRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCLPDKQTVTSLLRAGYKGRVTGWGNLRETW------IQPSVLQVVNLPIVERPVCKASTRIRITDNMFCAGFKVNDTKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSAGAGCDRKGKYGFYTHVFRLKRWIQKVIDQFG  246
                                    25        35 |      44        54      |60D|||||   65        75  |     84        94   |   103       113       123      |130       140       | -    |  155       165       175      184A  |||| 190       200    || 208       219  |    228       238        
                                               36A                      60A||||||||               77A                  97A                             129A||                148    150                               184A  ||||               204A|          217|  |                         
                                                                         60B|||||||                                                                     129B|                                                            186A|||                204B           219  |                         
                                                                          60C||||||                                                                      129C                                                             186B||                                 221A                         
                                                                           60D|||||                                                                                                                                        186C|                                                              
                                                                            60E||||                                                                                                                                         186D                                                              
                                                                             60F|||                                                                                                                                                                                                           
                                                                              60G||                                                                                                                                                                                                           
                                                                               60H|                                                                                                                                                                                                           
                                                                                60I                                                                                                                                                                                                           

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3HK3)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HK3)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THRB_MOUSE | P19221)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0070053    thrombospondin receptor activity    Combining with thrombospondin and transmitting the signal to initiate a change in cell activity.
biological process
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0048712    negative regulation of astrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of astrocyte differentiation.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0032967    positive regulation of collagen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:1900738    positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of phospholipase C-activating G-protein coupled receptor signaling pathway.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:2000379    positive regulation of reactive oxygen species metabolic process    Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0051281    positive regulation of release of sequestered calcium ion into cytosol    Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051480    regulation of cytosolic calcium ion concentration    Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0014854    response to inactivity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inactivity stimulus.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0070493    thrombin-activated receptor signaling pathway    The series of molecular signals generated as a consequence of a thrombin-activated receptor binding to one of its physiological ligands.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        THRB_MOUSE | P192212ocv 2pux 2pv9 3edx 3hk6 3hki

(-) Related Entries Specified in the PDB File

1tq0 THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A HAS A COLLAPSED PRIMARY SPECIFICITY POCKET
3hk6 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A (TWO MOLECULES IN THE ASYMMETRIC UNIT)
3hki CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A IN COMPLEX WITH THE EXTRACELLULAR FRAGMENT OF HUMAN PAR1
3hkj CRYSTAL STRUCTURE OF HUMAN THROMBIN MUTANT W215A/E217A IN COMPLEX WITH THE EXTRACELLULAR FRAGMENT OF HUMAN PAR1